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Detailed information for vg1216930858:

Variant ID: vg1216930858 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16930858
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.32, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGATCAGTGGAGATTTAATGTTACTTTAATTACTCAATTGTTTTACTGTTTGCTCAATAAAATGTTTTACAGCCGCCTTTATGCAAATAGCCACAAAC[T/C]
GTCCTTGTGTTCCCCTTGCACGTCTGCATCGTTGGTGTGGCTTGCTGAGTACGGTGGTTGTACTCAGCCTTGCTATTATTCCCCCTTTTCAGAAGTGCAG

Reverse complement sequence

CTGCACTTCTGAAAAGGGGGAATAATAGCAAGGCTGAGTACAACCACCGTACTCAGCAAGCCACACCAACGATGCAGACGTGCAAGGGGAACACAAGGAC[A/G]
GTTTGTGGCTATTTGCATAAAGGCGGCTGTAAAACATTTTATTGAGCAAACAGTAAAACAATTGAGTAATTAAAGTAACATTAAATCTCCACTGATCAAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.20%	6.40%	25.16%	17.22%	NA
All Indica	2759	36.90%	8.30%	28.45%	26.39%	NA
All Japonica	1512	73.50%	2.90%	19.64%	3.97%	NA
Aus	269	65.10%	5.90%	23.79%	5.20%	NA
Indica I	595	40.50%	8.20%	15.46%	35.80%	NA
Indica II	465	29.20%	4.10%	42.58%	24.09%	NA
Indica III	913	32.10%	12.50%	30.89%	24.53%	NA
Indica Intermediate	786	44.10%	6.00%	27.10%	22.77%	NA
Temperate Japonica	767	94.80%	0.10%	2.87%	2.22%	NA
Tropical Japonica	504	37.10%	8.30%	48.02%	6.55%	NA
Japonica Intermediate	241	81.70%	0.40%	13.69%	4.15%	NA
VI/Aromatic	96	65.60%	11.50%	20.83%	2.08%	NA
Intermediate	90	58.90%	4.40%	25.56%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216930858	T -> C	LOC_Os12g28630.1	upstream_gene_variant ; 1799.0bp to feature; MODIFIER	silent_mutation	Average:17.976; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg1216930858	T -> C	LOC_Os12g28620.1	downstream_gene_variant ; 3906.0bp to feature; MODIFIER	silent_mutation	Average:17.976; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg1216930858	T -> C	LOC_Os12g28640.1	downstream_gene_variant ; 505.0bp to feature; MODIFIER	silent_mutation	Average:17.976; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg1216930858	T -> C	LOC_Os12g28630-LOC_Os12g28640	intergenic_region ; MODIFIER	silent_mutation	Average:17.976; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg1216930858	T -> DEL	N	N	silent_mutation	Average:17.976; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216930858	3.14E-06	NA	mr1063	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1216930858	6.59E-07	NA	mr1329	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1216930858	2.40E-06	2.40E-06	mr1329	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251